The nucleosomes are the basic organizational units of all eukaryotic chromatin. Knowledge of their detailed molecular structure and interactions of their proteins with DNA is necessary for an understanding of gene control processes in normal and cancerous human cells. Although nucleases have been used to obtain most of the information so far available on nucleosome structure, their use also introduces numerous problems in interpretation due to their DNA sequence site-specificity. The present work has shown that the nucleolytic compound, methidium-propionyl-EDTA(Fe2+) (MPE) exhibits essentially complete neutrality with respect to cleavage of primate alphoid DNA sequences, the most abundant repeat sequences in primate, including human, genomes. The sequences, when packaged in nucleosomes, are cleaved at different locations from those that are attacked by nucleases, the classical reagents for probing chromatin structure. This altered pattern extends into the nucleosome linker regions as well as the core. The experiments indicate that particular DNA dinucleotides, notably AA and TT, are of special importance in imposing restrictions on the spatial positioning of adjacent nucleosomes and cores. Work is continuing with MPE to obtain DNA footprints of the exact contact points of the nucleosomal proteins with specific DNA sequences as revealed by direct DNA sequencing. The transcription in vitro and in vivo of a family of long-interspersed DNA sequences, first identified in KpnI digests of human DNA and termed the KpnI family in this laboratory, has been studied. The strategic location of these sequences near genes that are developmentally regulated, their active transcriptional properties, and their permuted linear arrangements are consistent with the hypothesis that these sequences may act as gene regulatory elements in human cells. This work has shown that the sequences are transcribed in human cells by RNA polymerase II, that both complementary strands of the DNA helix are transcribed, and that the sequences exhibit tissue-specific transcriptional patterns characteristic for each differentiated human cell of a specific type. One KpnI-like element has been newly identified and is of particular interest because it contains, within a longer sequence, sequences homologous to a 7S DNA that is distinct from 7S K and 7S L RNAs and appears to be a new 7S RNA species. This element shows the strongest differential patterns of transcription with different highly specialized human cells (hemoglobin and immunoglobulin producing cells, fibroblasts, neurobastoma, and hepatoma). The complete nucleotide sequence determination and cloning of the new 7S RNA from cDNA libraries is now in progress. (I)